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RiboSeq Profiling QC Specifications

Process Details

  • Name: RiboSeq Profiling QC
  • Process UUID: ayk0svbihne79c9y0rza8wm3re3o8x
  • Process Group: ribosome_profiling

Overview

This process performs comprehensive quality control analysis for ribosome profiling (Ribo-seq) sequencing data. It generates detailed QC metrics including read distribution patterns, fragment size analysis, P-site positioning, and strand specificity to assess the quality of ribosome profiling experiments and guide downstream analysis decisions.

This process is implemented in Perl, which invokes an R script for ribosome profiling quality control analysis using the ribosomeProfilingQC package.

Key Functionality

  • Read Distribution Analysis: Analyzes the distribution of ribosome-protected fragments relative to start and stop codons to assess P-site positioning accuracy
  • Fragment Size Profiling: Determines the optimal fragment length for ribosome footprints and identifies the most abundant read lengths
  • Strand Specificity Assessment: Evaluates the strandedness of sequencing reads to ensure proper library preparation and alignment
  • P-site Coordinate Mapping: Calculates precise P-site coordinates for ribosome positioning analysis

Input/Output Specification

Inputs

Required Inputs

  • bamFile

    • Description: Aligned ribosome profiling sequencing reads
    • Format: BAM file

  • bam_index

    • Description: Index file for the BAM alignment file
    • Format: BAI file

Outputs

  • outputHTML
    • Description: Comprehensive quality control report containing read distribution plots, fragment size analysis, P-site positioning metrics, and strand specificity assessment
    • Format: HTML file

References & Resources

  • Tool Documentation: Contact the team for details on ribosomeProfilingQC
  • Related Papers: Calviello, L., et al. (2016). Detecting actively translated open reading frames in ribosome profiling data. Nature Methods, 13(2), 165-170. DOI: 10.1038/nmeth.3688